Contacts of the strand formed by residues 21 - 26 (chain K) in PDB entry 2YHT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 21 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C LYS* 6.4 2.0 - - + -
19K ARG 3.4 9.6 - - - +
20K VAL* 1.3 89.1 - - + +
22K VAL* 1.3 58.5 + - - +
34K GLY 3.6 11.0 - - - +
35K GLN* 4.5 8.5 - - + +
65K SER* 2.7 48.2 + - - +
66K ARG* 3.7 14.6 - - - +
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Residues in contact with VAL 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 3.8 37.7 - - + -
20K VAL 3.3 14.1 + - - +
21K PRO* 1.3 76.6 - - - +
23K SER* 1.3 65.1 + - - +
24K ILE* 4.3 9.4 - - + -
33K GLN* 3.4 7.4 - - - +
34K GLY 2.8 40.3 + - - +
36K ILE* 4.0 20.0 - - + +
46K LEU* 3.8 19.7 - - + -
62K VAL* 4.6 3.6 - - + -
63K VAL 3.6 8.1 - - - +
64K PRO* 4.1 5.8 - - + -
65K SER* 5.3 1.1 - - - -
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Residues in contact with SER 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 5.5 0.3 + - - -
22K VAL* 1.3 73.4 - - - +
24K ILE* 1.3 61.5 + - - +
25K TYR* 3.8 2.3 + - - +
31K LYS* 3.0 46.6 + - - -
32K LEU 3.3 4.3 - - - -
33K GLN* 3.2 15.6 + - - +
61K THR 3.8 0.3 - - - +
62K VAL* 3.7 0.5 - - - -
63K VAL* 2.8 51.2 + - - +
65K SER* 6.1 0.5 - - - -
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Residues in contact with ILE 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K VAL* 4.0 12.7 + - + -
23K SER* 1.3 73.4 - - - +
25K TYR* 1.3 62.9 + - - +
26K LEU* 3.8 10.1 + - + -
30K ILE 3.8 0.2 - - - +
31K LYS* 3.5 2.4 - - - -
32K LEU* 2.7 46.3 + - + +
36K ILE* 5.0 2.7 - - + -
44K ILE* 4.4 18.6 - - + -
46K LEU* 3.7 37.9 - - + -
54K VAL* 4.5 9.6 - - + -
59K ILE* 3.6 41.1 - - + -
61K THR 3.7 2.5 - - - -
62K VAL* 4.6 13.0 - - + +
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Residues in contact with TYR 25 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ASN 4.2 13.5 - - - -
28E ASN* 2.4 32.0 + - + -
23K SER 3.8 2.3 + - - +
24K ILE* 1.3 71.9 - - - +
26K LEU* 1.3 58.1 + - - +
29K GLY* 3.2 26.0 - - - -
30K ILE 3.8 2.7 - - - -
31K LYS* 4.0 23.3 - - + -
59K ILE* 3.6 4.7 - - - +
60K SER* 2.8 48.3 + - - -
61K THR* 2.8 38.5 + - + +
63K VAL* 5.5 1.8 - - + -
26L LEU* 4.3 11.0 - - + -
28L ASN* 3.5 22.8 + - - -
30L ILE* 4.2 11.9 - - + +
32L LEU* 5.8 1.3 - - + -
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Residues in contact with LEU 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J SER* 4.0 22.4 - - - +
61J THR* 4.9 3.6 - - + -
24K ILE* 4.3 4.3 - - + -
25K TYR* 1.3 85.6 - - - +
27K VAL* 1.3 60.2 - - + +
28K ASN* 3.1 16.2 - - - +
29K GLY* 2.9 21.3 + - - -
30K ILE* 2.8 27.2 + - + +
32K LEU* 3.7 35.0 - - + -
54K VAL* 3.9 24.0 - - + -
58K ALA* 3.3 25.1 - - + +
59K ILE* 4.0 6.3 - - + -
60K SER* 3.8 2.4 + - - -
28L ASN* 3.9 0.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il